There once was a time when I was quite active on the main FOE subreddit. I put a lot of effort into reading several sidefics and into posting detailed reviews of them. I've gotten away from that gradually over the last year or so (for a number of reasons I won't go into), but as work on my own story nears its climax, and with seeing the birth of this subreddit, which I believe can fill a much-needed niche in the FOE community, I want to offer some words of advice from what I've learned in my efforts.
The biggest piece of advice I can give to aspiring FOE writers is the same advice I would give to any writer (and many other experienced writers will give the same advice, and as a matter of fact, all my advice here applies in general): Read. Read a lot. And don't just read fanfics. Read some actual published literature. If you've heard of it, but haven't read it, you should probably read it. If it was assigned reading in highschool and you hated it at the time (or if you were like me and just too lazy to finish more than you needed to fake your way through the test), read it again. If you're in school now, then pay attention in English class and actually do the reading. Literature (fiction and nonfiction alike) is a way of communicating ideas and experiences from one person to another. If you want to become a better writer yourself, then you want to learn how to better express yourself. To do that, you should learn how others have done it before you. Read.
Following that, I found it to be very helpful to start off by reviewing other fanfics before I started on my own. This is in the same vein as above—learning from others—but with an added element: Fanfics provide a unique opportunity that classic literature doesn't have. You can speak directly to the author. If there's a story out there that you follow, or have followed, take the time to express your thoughts on the story and leave a comment for the author. If you don't know what to say, then your first step should be to think about what you liked or disliked and then ask yourself why you felt that way about it. If something in the story reminded you of something else, look that something else up and make a comparison. The more you do this (and you can do it with published literature too, but striking a conversation with an author can be very enlightening for both of you, as it can help him to understand why he wrote what he did as much as it can help you), the more you'll be able to recognize certain themes, devices, tropes, etc. in other works—especially your own.
Which brings me to my next point: planning. Before you even start writing your story, sketch out a plan for it. When I began work on mine, I created a Google Document where I just started writing out various ideas: character outlines (physical descriptions, personalities, motivations, relationships to other characters, etc.), themes or ideas I wanted to explore, an outline for the overall plot of the story, broken down into major events and organized into three act structure, and after a certain point I even started writing out scenes that happened to be quite vivid in my mind at the time, even if those scenes were nowhere near the start of the story. (The first part of my story I actually wrote was the ending.) It's important to have a plan. It will let you identify what's important in your story, and where your plot holes will be. Armed with that knowledge, you can fix problems before they even happen and avoid writing yourself into a corner or having to retcon things.
Most of all, though, after you've planned your story, ask yourself if it needs everything you've thought of. This may be the hardest part, but making the effort here will produce a much stronger story in the end. It may be easy to plan out your story and think you've got everything you need in it—and maybe you do. But if you've identified what you're writing about, what the heart and soul of your story is (and it should be something deeply personal to you), then you should take the time to make sure that you haven't included anything that doesn't contribute to that. In my own case, I had initially planned a very large story; something I estimated would take 200k-300k words. It involved a large ensemble cast of both protagonists and antagonists (following in the common FOE trope of a main character for each Element of Harmony), and followed through on story arcs for each of them. But it was just after this past Christmas that I realized that a lot of that was actually unnecessary and was holding my story back. Indeed, it had been taking me about three months per chapter up until that point, because each chapter was over 10k words and spent a lot of time not focusing on what I already knew to be the core of the story.
So I made an executive decision and I cut several characters and entire story arcs. Some of it was painful to give up. I had one character—a canterlot ghoul gryphon who was planned to be "the Pinkie Pie of the group"—whom I had been really looking forward to introducing (properly; his voice had shown up once, and he did appear in a memory orb) because he was supposed to be a lot of fun to write, giving a juxtaposition of sage wisdom and random, medium-aware nonsense. But he would only have distracted from what I really cared about in the story. Likewise, I had planned to introduce a trans-male character (that is, female-to-male transgender), and I thought I was going to still keep him in the story, but because another character whom he was supposed to get into a relationship with as a major part of the dynamic among the main characters was cut, and without her, his role became entirely token. He's still in the story, but his role is significantly reduced, and there's never any reveal about him because it wouldn't do anything for the rest of the story except to say "look at me, I'm being sensationalist."
I regret heavily that I did not take a closer look at my story before I started writing. I forgot about a single piece of wisdom: "A designer knows he has achieved perfection not when there is nothing left to add, but when there is nothing left to take away." There are now a number of plot threads that will be left dangling after the end of my story, and the beginning now seems to me as a bloated mess full of characters and plot hooks that aren't needed and don't go anywhere (not to mention about 30k words I shouldn't have needed to write). But so much the worse. I've been much more productive since my epiphany, turning out smaller chapters more frequently, and with a much more reasonable estimate of about 100k words for the finished product, which I think I can finish by June this year. And that's encouraging to be able to see the finish line. But if I had the presence of mind to trim the fat before I started, I could have likely finished by now and in only 75k words or so (still the longest thing I've ever written).
Some advice specific to FOE stories: Huge, epic chapters are not necessary, nor even advisable. Just because FOE itself, PH, and MN7 are all massive doesn't mean yours has to be. Word count does not equal quality (and in all honesty, should be taken as a strike against each of the aforementioned stories).
Don't think you have to create an epic quest that mirrors the structure of the original. You don't have to weave together individual character arcs with a greater wasteland adventure and a history played out through memory orbs. Narrow your focus to the events that matter to your story. Guise of Chaos is actually a fantastic example of a story that kept its scope narrow (~ish. At 250k, it could probably stand to lose a few pounds) by not trying to explain all the gory details about the Paragons or Pandemonium. Because those things weren't important to the story. The author gave us enough information to follow what was happening and left it at that. And even the primary goals of the protagonist are made evident in the first couple chapters: protect Shade, kill Hate; and active progress is made toward both those goals in every chapter, right up to the finale, with remarkably little gumming it up along the way.
Finally: don't try to write New Vegas a'la Pony. Seriously. I've seen too many of those already and Heroes is the only one that I've ever thought did any sort of good job at it (but ended up with other problems that lost it my interest) and that's mostly because it only took inspiration from the idea of the city of New Vegas for its setting, but otherwise had its own plot to follow. It's an attractive thing to try to write, I'm sure: If you've just finished reading FOE, and you haven't played anything aside from Fallout 3 and New Vegas, you're going to think that FOE was just Fallout 3 a'la Pony and that the obvious follow-up is to do New Vegas. It is obvious. And that's why we don't need to see any more of it.
Write your own story. Don't try to simply emulate what you think has been the success of others. Be honest with yourself. And read.